10-88660884-G-C

Variant names:

• chr10-88660884-G-C
• rs1214451

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.555 in 151,830 control chromosomes in the GnomAD database, including 24,014 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.56 (24014 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.444
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84224 AN: 151712 Hom.: 23973 Cov.: 31

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.587

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.555 AC: 84320 AN: 151830 Hom.: 24014 Cov.: 31 AF XY: 0.562 AC XY: 41660 AN XY: 74184

African (AFR) AF: 0.608 AC: 25183 AN: 41402

American (AMR) AF: 0.606 AC: 9238 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2060 AN: 3470

East Asian (EAS) AF: 0.890 AC: 4610 AN: 5178

South Asian (SAS) AF: 0.661 AC: 3183 AN: 4812

European-Finnish (FIN) AF: 0.485 AC: 5079 AN: 10478

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33185 AN: 67934

Other (OTH) AF: 0.591 AC: 1242 AN: 2100

Alfa AF: 0.359 Hom.: 969

Bravo AF: 0.567

Asia WGS AF: 0.794 AC: 2760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.52
PhyloP100		-0.44

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1214451; hg19: chr10-90420641;